Computer and Information SciencesBlogger

iPhylo

Rants, raves (and occasionally considered opinions) on phyloinformatics, taxonomy, and biodiversity informatics. For more ranty and less considered opinions, see my Twitter feed.
ISSN 2051-8188. Written content on this site is licensed under a Creative Commons Attribution 4.0 International license.
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Published

DataCite have released the Data Citation Corpus, together with a dashboard that summarises the corpus. This is billed as: The goal is to build a citation database between scholarly articles and data, such as datasets in repositories, sequences in GenBank, protein structures in PDB, etc. Access to the corpus can be obtained by submitting a form, then having a (very pleasant) conversation with DataCite about the nature of the corpus.

Published

A quick note to support a recent Twitter thread https://twitter.com/rdmpage/status/1729816558866718796?s=61&t=nM4XCRsGtE7RLYW3MyIpMA The article “Diversification of flowering plants in space and time” by Dimitrov et al. describes a genus-level phylogeny for 14,244 flowering plant genera. This is a major achievement, and yet neither the tree nor the data supporting that tree are readily available.

Published

This blog post documents my attempts to create links between two major resources for plant taxonomy: JSTOR’s Global Plants and GBIF, specifically between type specimens in JSTOR and the corresponding occurrence in GBIF. The TL;DR is that I have tried to map 1,354,861 records for type specimens from JSTOR to the equivalent record in GBIF, and managed to find 903,945 (67%) matches. Why do this? Why do this?

Published

Recently I’ve been messing about with DNA barcodes. I’m junior author with David Schindel on forthcoming book chapter Creating Virtuous Cycles for DNA Barcoding: A Case Study in Science Innovation, Entrepreneurship, and Diplomacy, and I’ve blogged about Adventures in machine learning: iNaturalist, DNA barcodes, and Lepidoptera. One thing I’ve always wanted is a simple way to explore DNA barcodes both geographically and phylogenetically.

Published

To much fanfare BiCIKL launched the “Biodiversity Knowledge Hub” (see Biodiversity Knowledge Hub is online!!!). This is advertised as a “game-changer in scientific research”. The snappy video in the launch tweet claims that the hub will it will help your research thanks to interlinked data… …and responds to complex queries with the services provided… Interlinked data, complex queries, this all sounds very impressive.

Published

Recently I’ve been working with a masters student, Maja Nagler, on a project using machine learning to identify images of Lepidoptera. This has been something of an adventure as I am new to machine learning, and have only minimal experience with the Python programming language. So what could possibly go wrong?

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